I don't think so. If you listen to the lyrics closely there is no connection made at all.

Plus I don't believe she ever was on the island. People make the connection because she mentions San Pedro. If you watch her video for the song... her and San Pedro... she's obviously thinking about something other than the town or island.

I had the same question and did a search on this topic last year. This quote: "Her song "La Isla Bonita" (1986) was inspired by a visit she made to San Pedro, Ambergris Caye, Belize, with her then-husband Sean Penn," appears on several Madonna websites. I never could find anything else to substantiate that she and Penn had been to Belize. The video for the song was filmed at a castle in Spain, but Spain does not fit the "tropical" references in the song, so I still like to believe San Pedro inspired the lyrics.